Why not just have WvW become a megaserver like thing where we do away with server identities altogether and have a constant Red/Blue/Green faction sort of matchup? Have guilds picks between the three colors and boom. You've also added GvG on accident.
Make some kind of mist instability lore reason that sometimes guilds will get their color changed out from under them to combat stacking and other forms of manipulation/to balance out colors that are over or under picked for a season.
This instability will only affect guilds so many times so often before the algorithm is forced to pick other guilds it hasn't happened to so often. After a set period guild will again be susceptible to color switch instability.
The entire games population can use the WvW maps and be appropriated to their proper color in megaserver multimaps and all these instances wins/loses can add to the overall score. Winning color guild players get really cool neato mist bonuses they can take back into PvE.
Ergo basically the old world WvW bonuses but on a color win. Or something along those lines.
Players of the same guild get thrown into the same instance, they get que priority to said instance. Unaffiliated/guildless players will have to choose a side every new matchup and be locked into it.
They don't get cool bonuses because they're guildless losers/should be encouraged to join a guild but can still enjoy WvW as they see fit... or if they're smart they'll just use their friend/guild bank and get the bonuses like that and not be guildless losers!
Just a randumb idea for WvW I've had rattling around in my heard for a while now. If this isn't new or very good I apologize. If there's something to it and you want to add some much needed polish to the concept, please do.